A proteomic portrait of dinoflagellate chromatin reveals abundant RNA-binding proteins
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Dinoflagellate chromatin is unique among eukaryotes, as the chromosomes are permanently condensed in a liquid crystal state instead of being packed in nucleosomes. However, how it is organized is still an unsolved mystery, in part due to the lack of a comprehensive catalog of dinoflagellate nuclear proteins. Here, we report the results of CHromatin Enrichment for Proteomics (CHEP) followed by shotgun mass spectrometry sequencing of the chromatin-associated proteins from the dinoflagellate Lingulodinum polyedra. Our analysis identified proteins involved in DNA replication and repair, transcription, and mRNA splicing, and showed a low level of contamination by proteins from other organelles. A limited number of proteins containing DNA-binding domains were found, consistent with the lack of diversity of these proteins in dinoflagellate transcriptomes. However, the number of proteins containing RNA-binding domains was unexpectedly high supporting a potential role for this type of protein in mediating gene expression and chromatin organization. We also identified a number of proteins involved in chromosome condensation and cell cycle progression as well as a single histone protein (H4). Our results provide the first detailed look at the nuclear proteins associated with the unusual chromatin structure of dinoflagellate nuclei and provide important insights into the biochemical basis of its structure and function.
KeywordsDinoflagellate Nucleic acid-binding protein Chromatin Proteomics
Proteomics analyses were performed by the Center for Advanced Proteomics Analyses, a Node of the Canadian Genomic Innovation Network that is supported by the Canadian Government through Genome Canada. Computer-intensive analyses were made on the supercomputer Guillimin at McGill University, managed by Calcul Québec and Compute Canada. The operation of this supercomputer is funded by the Canada Foundation for Innovation (CFI), the ministère de l’Économie, de la science et de l’innovation du Québec (MESI), and the Fonds de recherche du Québec - Nature et technologies (FRQNT). We are grateful to Dr. F. van Dolah for the anti-PCNA antibody. We thank Drs. Annie Angers, James Omichinski, and William Zerges for their extensive review of this manuscript.
This study was funded by the National Science and Engineering Research Council of Canada (NSERC) through an Alexander-Graham-Bell Canada Doctoral Scholarship awarded to M. B. and an NSERC Discovery research grant awarded to D. M. (number 171382-03).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no competing interests.
This article does not contain any studies with human participants or animals performed by any of the authors.
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